Existing methods of interrogating a biological system can derive significant amounts of information. Examples of existing methods include methods for determining an organism's genome, exome, transcriptome, proteome, and metabolome.
The genome can be solved in order to determine an organism's genetic material, typically in the form of DNA (though RNA serves a similar purpose in a subset of organisms). The genome can include all of the genes stored within the genetic material. The exome is a part of the genome that is formed by exons.
The transcriptome refers to the level of expression of mRNA for a cell, a group of cells, or an entire organism. The transcriptome contains some information regarding the environment for a particular cell line, because the mRNA expression products can vary based on environmental conditions.
The proteome refers to the populations of proteins expressed in a cell, a group of cells, or an entire organism. The proteome also contains information regarding the environment for a particular cell line, because protein expression can vary based on environmental conditions.
The metabolome refers to the population of small-molecules present in a biological sample. The metabolome contains additional and different information regarding the environment for a particular cell line, because small-molecule generation and consumption can vary based on environmental conditions.
Beyond all of the above lies an area that has yet to be effectively or efficiently probed, namely the “conformatiome”, which refers to the conformational information for any or all of the biological molecules in a given biological sample. The conformatiome ideally provides conformational information regarding various biological molecules in their native and unaltered conformational state.
Current methods that claim to probe conformational structural information suffer from one or more of the following problems. First, some methods require crystallization of a sample (such as x-ray crystallography) or other manipulation that does not present the biological molecule in its native state. Second, some methods require the addition of non-native chemical species to a sample in order to provide species for tagging a sample. One example is fast photochemical oxidation of proteins (FPOP), which requires the addition of hydrogen peroxide to oxidize biological molecules. The addition of hydrogen peroxide may alter the conformational state of the biological molecules being studied. Third, some methods require immensely expensive equipment. For example, the aforementioned FPOP requires use of an excimer laser, which is an expensive instrument. Other methods, such as synchrotron-based hydroxyl radical footprinting, can involve use of multi-million dollar facilities such as a synchrotron.
A need exists for inexpensive systems and fast methods for studying the conformatiome, without the need to introduce the biological molecule(s) in question to foreign substances that might alter their structure.